PARN RNA-Seq in HepG2

General Information


RBP	PARN
Cell_Line	HepG2
Method	shRNA
Exp_Name	PARN-BGHLV20-HepG2
ENCODE_series_ID	ENCSR574UNC
Batch_ID	BGHLV20
Pool ID	Pool-150705
Local_Set_Name	set20
ENCODE_KD_Exp_ID	ENCSR825QXH
ENCODE_CN_Exp_ID	ENCSR305XWT
Rep1	PARN-BGHLV20-47_17730
Rep2	PARN-BGHLV20-48_17731
CN1	non-target-BGHLV20-1_17706
CN2	non-target-BGHLV20-2_17707
Rep1_qPCR	57.0
Rep2_qPCR	63.1
Rep1_WB	84.6
Rep2_WB	94.7
Antibody Cat#	GTX115020
Antibody Lot#	GTX115020
Antibody DCC ID	ENCAB392QEW
Status	Released
Project	ENCODE3
ID	500

Experiment Information (Status: Released)

	BGHLV20-47	BGHLV20-48
idx	411	412
TRCN#_or_BGC#	TRCN0000049744	TRCN0000049744
shRNA_or_gRNA_sequence	CCCAGACTCTTGGATACTAAA	CCCAGACTCTTGGATACTAAA
PAM
Name	PARN	PARN
Sample_ID	BGHLV20-47	BGHLV20-48
transduction_Date	10/2/2014	10/2/2014
days
RBP_name	PARN	PARN
qPCR_result	57.0	63.1
Ave_qPCR	60.0
RT-qPCR_primer-F	CCCTACACCCTGCAGAATCA
RT-qPCR_primer-R	GGCCAGCTTCCTCTTGACTA
protein_conc	3686	4136
WB_result	84.6	94.7
Ave_WB	89.6
WB_DONE_date	5/19/2015
MW	73kDa
IP	1	1
antibody_Cat#	GTX115020	GTX115020
Antibody DCC ID	ENCAB392QEW	ENCAB392QEW
submitted_to_DCC_date	8/6/2015
Rep1_TPM	24.7	0
Rep2_TPM	22.6	0
Action
Library_start_date	5/29/2015	5/29/2015
repeat_library
Note
ID	2480	2481

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PARN	Product_ID: GTX115020 Lot_ID: 40884 Source: GeneTex Target Name: PARN-human

Experiment Status

	BGHLV20-47	BGHLV20-48
Sample_ID	BGHLV20-47	BGHLV20-48
Sample Name	PARN-BGHLV20-47_17730	PARN-BGHLV20-48_17731
Sample Name	PARN-BGHLV20-47_17730	PARN-BGHLV20-48_17731
RBP	PARN	PARN
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-11	2015-08-11
Project	ENCODE3	ENCODE3
Note
ID	732	733

Library-Prep
Sequencing

Library-Prep Information

	BGHLV20-47	BGHLV20-48
Sample #
Sample Name	PARN-BGHLV20-47	PARN-BGHLV20-48
Sample_Name_Alias	PARN-BGHLV20-47_17730	PARN-BGHLV20-48_17731
Index Well Position	S01	S02
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-05-29	2015-05-29
Lib_ID	Lib-150529	Lib-150529
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV20-22-23/set1/A4.png	DNA_Library_LV20-22-23/set1/B4.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_LV20-22-24/set1/C10.png	RNA_Library_LV20-22-24/set1/D10.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV20-47	BGHLV20-48
RBP	PARN	PARN
Batch_ID	BGHLV20	BGHLV20
WB_result	84.600	94.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2418	2419

Sequencing Information

	BGHLV20-47	BGHLV20-48
Sample_ID	BGHLV20-47	BGHLV20-48
Sample Name	PARN-BGHLV20-47_17730	PARN-BGHLV20-48_17731
Pool ID	Pool-150705	Pool-150705
LocalServer_folder	set20	set20
total_reads	52,170,000	52,310,000
total_aligned_reads	46,170,478	46,094,784
unique_aligned_reads	43,496,798	43,418,526
percent_uniqueAligned	0.83375	0.83002
correlation_replicates	0.986119	0.986119
spikein_reads	236,962	207,462
percent_spikeins	0.00454	0.00397
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1186	1187

Data Submission Information

	BGHLV20-47	BGHLV20-47
ENCODE_alias	brenton-graveley:PARN-BGHLV20	brenton-graveley:PARN-BGHLV20-HepG2
ENCODE_accession	ENCSR825QXH	ENCSR574UNC
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV20-47	BGHLV20-47
Sample Name	PARN-BGHLV20-47_17730	PARN-BGHLV20-47_17730
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2915	6846

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	platform	read_length	run_type	paired_end	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
PARN-BGHLV20-47_17730_ATCACG_L004_R1_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1186	HiSeq2000	100	paired-ended	1				non-target-BGHLV20-1_17706_ATCACG_L001_R1_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R1_001.fastq.gz	ENCODE3	15614
PARN-BGHLV20-47_17730_ATCACG_L004_R2_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1186	HiSeq2000	100	paired-ended	2				non-target-BGHLV20-1_17706_ATCACG_L001_R2_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R2_001.fastq.gz	ENCODE3	15656
PARN-BGHLV20-47_17730_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1186					GRCh38	V40	PARN-BGHLV20-47_17730_ATCACG_L004_R1_001.fastq.gz,PARN-BGHLV20-47_17730_ATCACG_L004_R2_001.fastq.gz		ENCORE2	15698
PARN-BGHLV20-47_17730_Signal.Unique.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1186					GRCh38	V40	PARN-BGHLV20-47_17730/Aligned.sortedByCoord.out.bam		ENCORE2	15740
PARN-BGHLV20-47_17730_Signal.Unique.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1186					GRCh38	V40	PARN-BGHLV20-47_17730/Aligned.sortedByCoord.out.bam		ENCORE2	15782
PARN-BGHLV20-47_17730_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1186					GRCh38	V40	PARN-BGHLV20-47_17730/Aligned.sortedByCoord.out.bam		ENCORE2	15824
PARN-BGHLV20-47_17730_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1186					GRCh38	V40	PARN-BGHLV20-47_17730/Aligned.sortedByCoord.out.bam		ENCORE2	15866
PARN-BGHLV20-47_17730_quant.sf	ENCODE_DATA/set20/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1186					GRCh38	V40	PARN-BGHLV20-47_17730_ATCACG_L004_R1_001.fastq.gz,PARN-BGHLV20-47_17730_ATCACG_L004_R2_001.fastq.gz		ENCORE2	15908
PARN-BGHLV20-48_17731_CGATGT_L004_R1_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1187	HiSeq2000	100	paired-ended	1				non-target-BGHLV20-1_17706_ATCACG_L001_R1_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R1_001.fastq.gz	ENCODE3	15615
PARN-BGHLV20-48_17731_CGATGT_L004_R2_001.fastq.gz	ENCODE_DATA/set20/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1187	HiSeq2000	100	paired-ended	2				non-target-BGHLV20-1_17706_ATCACG_L001_R2_001.fastq.gz,non-target-BGHLV20-2_17707_CGATGT_L001_R2_001.fastq.gz	ENCODE3	15657
PARN-BGHLV20-48_17731_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1187					GRCh38	V40	PARN-BGHLV20-48_17731_CGATGT_L004_R1_001.fastq.gz,PARN-BGHLV20-48_17731_CGATGT_L004_R2_001.fastq.gz		ENCORE2	15699
PARN-BGHLV20-48_17731_Signal.Unique.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1187					GRCh38	V40	PARN-BGHLV20-48_17731/Aligned.sortedByCoord.out.bam		ENCORE2	15741
PARN-BGHLV20-48_17731_Signal.Unique.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1187					GRCh38	V40	PARN-BGHLV20-48_17731/Aligned.sortedByCoord.out.bam		ENCORE2	15783
PARN-BGHLV20-48_17731_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1187					GRCh38	V40	PARN-BGHLV20-48_17731/Aligned.sortedByCoord.out.bam		ENCORE2	15825
PARN-BGHLV20-48_17731_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set20/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1187					GRCh38	V40	PARN-BGHLV20-48_17731/Aligned.sortedByCoord.out.bam		ENCORE2	15867
PARN-BGHLV20-48_17731_quant.sf	ENCODE_DATA/set20/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1187					GRCh38	V40	PARN-BGHLV20-48_17731_CGATGT_L004_R1_001.fastq.gz,PARN-BGHLV20-48_17731_CGATGT_L004_R2_001.fastq.gz		ENCORE2	15909